Alpha
by TTFshaunmichael
Summary: I've been thrown into the Mass Effect universe and I'm an experiment of Cerberus. The Illusive Man is as egotistical as I thought he would be. At least I'm not going through this alone, I've got Alpha with me. I woke up in a Cerberus base with a geth intelligence inside my head. What am I supposed to do? Guess I'll try to save as many people as I can. OC self-insert
1. Chapter 1

**A/N: First I love the Mass Effect series in my opinion it's one of the best series out there in gaming. This is my first attempt at a Mass Effect story so I hope all of you enjoy it. If I missed anything feel free to tell me. Constructive criticism is appreciated.**

_'Text' Is conversation in the head or thoughts  
_

"Text" Regular conversation

* * *

_I don't know where I am, everything's so dark. Why is it so dark? I can't see anything around me not even my hands. Where the hell am I?! Wait I can hear something, it sounds like a buzzing noise. What is that noise? How is this happening? I went to bed and I woke up here, where the hell am I? Why is this happening? _

A bright light envelops the room, and I cover my eyes since they were not used to it anymore. I slowly open my eyes trying to get a feel for my surroundings and see a man and a woman looking at me.

"How is he faring Ms. Lawson?" _That voice why does it sound so familiar? _My eyes slowly began to make out the two, but my vision was still blurred.

"His body was rejecting the implants at first, but now he has been fully integrated. He will be the ultimate soldier on the battlefield." _Implants? Soldier? Why are they saying I will be a soldier? God why does that voice sound so familiar? _

My vision became clearer, but something was off. I wasn't seeing normally it looked like there was some sort of HUD everywhere I looked. I tried to get a closer look at the two and my vision zoomed in._ My vision zoomed in? That can't be normal, maybe this is a dream? _As I saw the two I couldn't believe my eyes it was Miranda Lawson and the Illusive Man in the flesh. _Now I know I have to be dreaming, Mass Effect is just a game it's not real. But why does everything look so real and lifelike, if this is a dream it's the most realistic dream I have ever had in my life. _

"Will he comply with orders?" TIM asked inquisitively "We can't have him out in the field if he isn't loyal." _If you're talking about me you're god damn right I'm not going to be loyal to you. You're a fucking psychopath!_

"Yes I believe the geth implants in him will keep him loyal to you." _Wait geth implants? They combined me with a geth? First, that's fucking awesome. Now that I got that part out of the way, what the hell?! I'm human not some tool be used for TIM's benefit. Maybe if I just close my eyes I'll wake up in my bed. Nope didn't work, god damn I'm in the Mass Effect universe. First off this is so freaking awesome, second where the hell is Rob he would love this, third I'm going to fucking die here._

"That is all Ms. Lawson; you may continue your work on the Commander." Miranda walked away leaving me alone with TIM. He slowly walked up to me and eyed my body as if to make sure I was in perfect condition for him to use. I tried to speak, but no words came out of my mouth. He noticed this, "I see you're awake Mr. Michaels that saves me the trouble of doing it myself. Now I'm sure that you're wondering why you cannot speak it is because we removed your vocal chords. However I'm told that you can speak by thought now. I'll leave you do that."

* * *

_Speak by thought really? If I could do that you would have heard me cursing you the moment you walked in this room. Calm down, breathe, wait do I even need to breathe anymore. Ok freak out, done over with. I'm some type of combination between a geth and a human maybe I can control it. _

'_Hello? Any geth intelligence in my head right now?' _

'_We can hear you Mr. Michaels.' Great creepy synthetic voice in my head. 'As we just said Mr. Michaels we can hear you.' _

'_Oh sorry just not used to having voices in my head, no matter how many times I've joked about it before. I'm rambling and off topic great. So what's your name?' _

'_We do not require such a thing Mr. Michaels.' _

'_You can call me Shaun from now on and I can't very well speak to you if you don't have a name. Do you mind if I give you a name?' _

'_If you wish to do so Shaun we will reply by the designation that you give us.' _

'_Great let's see how about Alpha?' _

'_That is an acceptable designation, Revelation 22:13 I am the Alpha and the Omega, the First and the Last, the Beginning and the End.'_

'_Thought you would like it, so this whole sharing a body thing how exactly does it work?' _

'_TIM wishes for us to work together in order to be the perfect soldier. The advanced intellect of a machine and the instincts of a human, he believes together we can be on par to Commander Shepard.' _

'_Right so about that? Just to clarify we share a body and a mind. Correct?'_

'_You are correct in your statement.'_

'_Do we share memories?'_

'_If you choose to share them then yes we will be able to see everything you have once seen.'_

'_Ok I'm going to show you something, and hopefully you won't take me over.' _I open my mind for Alpha so that he can see everything I have. All of my knowledge of what can happen in this universe. I can see everything in flashes of images appearing in my mind.

'_Different dimension travel does not seem probable.' _

'_Yeah you would think so, but I'm proof of it. Also in my world there was never any experiment to combine human and geth.' _

'_Perhaps there was it is possible that it may have been going on behind the scenes.' _

'_Yeah I guess you're right so where does this leave us?' _

'_You have shown us what is to come. The Reapers are coming to destroy all of humanity, and in doing so they will enslave the geth. We do not wish this to occur we will stop this with your help.' _

'_Great that means we will be working together from now on. Hopefully I can get back home, but until then I'm going to make sure everyone is safe.' _

'_We will help you Shaun, but first the most logical step is to wait for Commander Shepard to awaken. We have hacked into the security systems of this base and it seems as if Commander Shepard has yet to be revived.' _

'_Ok so we wait until he wakes up and escape in the chaos, but what's stopping Miranda from shooting us when we try getting on the shuttle.'_

'_TIM will want us to be with Shepard, it is in high probability that we were made in order to assist Shepard in the impending suicide mission. Correction: Commander Shepard in this dimension is a female.'_

'_Alright so we'll wait till she wakes up, but until then I need to learn how to fight.' _

'_We estimate it will be six months before Commander Shepard awakens. We believe TIM will put you through multiple training simulations before she awakens. We will assist you in every way that we can.' _

* * *

Wow so this is really happening I'm in the Mass Effect universe, I've been implanted with geth intelligence and had several upgrades to my body. As far as I can tell I'm still mostly human except for the HUD, Alpha, and the fact that I can make metal plating appear from my skin yeah mostly human. God this is so weird, but what am I going to do? Maybe I'll go back to my world if I beat the game, wait I probably have to go all the way to the ending of Mass Effect 3. Maybe I can save Shepard?

* * *

I duck behind cover as bullets start whizzing past my head. It's been three months since that asshole TIM has been giving me combat training and I've been doing fairly fine. At least I think so, granted my idea of fine is not getting shot. Alpha has been very helpful in all of the simulations, and our teamwork has gotten pretty good since we began. At first he had to take control sometimes, but after I got the swing of things he has taken more of a supportive role. I've been hiding behind this box for too long it's time to end this.

'_Alpha how many hostiles left?' _

'_There are currently three LOKI mechs and two FENRIS mechs left.' _

'_We only have three bullets left in this gun since TIM wanted to see what we could do in a situation like this. Alright we'll use the bullets to finish the three LOKI mechs off with a single shot to the head, and I'll think of something for the other two. Can you draw up the trajectories for me?'_

'_We anticipated your attack plan and have already finished the trajectories for you. Whenever you are ready we will be able to execute your plan of attack.' _

'_God I'm glad I have you to back me up. Alright let's do this Alpha.' _

I stood up from behind the box that I was using to take cover and spotted the two FENRIS mechs. One of them was trying to take me from the left side while the other the right, and in front of me were the LOKI mechs preparing to fire. I quickly fired off two precise shots into the heads of two of the mechs and they quickly exploded after. The final mech hid behind the barrier before I could fire the final shot.

'_Shaun we have drawn a new trajectory that will ricochet the bullet into the LOKI mech's main power source it is currently on your HUD.' _

'_Alpha I love you.' _

'_We have no response to your statement.' _

I fired the final shot into the trajectory that Alpha had laid out before me and the final LOKI mech exploded. I saw the two FENRIS mechs closing in and knew they would be on me in a couple of seconds. Looks like I'll have to use it, I hit my knuckles together and used overload to form an electric current through both my fists and slammed the two FENRIS mechs into the ground.

'_That fucking hurt!' _

'_We have advised you against using that technique, until we acquire better plating for our metal skin it will cause you some harm.' _

'_Well what would you have done?' _

'_We would have noticed that you dropped the spare and that it is currently under your foot.' _I lift up my foot to see a spare thermal clip stuck to the bottom of my boot. I hit my head with the palm of my hand.

'_Why did you not tell me about it sooner?' _

'_We wished to see what you would do in the situation.' _

'_You know sometimes you're just as bad as TIM.'_

'_We take offense to that statement, we thought you loved us.' _

'_Yeah, yeah, yeah Alpha. God the more that you look into my mind the more of a smartass you become.'_

'_We are learning from your memories, what is the saying? We learned from the best.' _

'_Close enough.' _

"That was very impressive work Mr. Michaels, such a unique way of using overload." TIM said over the speaker. I wish I could talk so I could curse him. "Report to Ms. Lawson, she would like to run some more tests on you." _I made my way to Miranda's lab since I can't argue back since I don't have any freaking vocal chords! _

I entered Miranda's lab to find that she was not there. I decided now would be a good time to look around. _'Hey Alpha keep a lookout for me while I look around.' _I was so happy when Alpha hacked all the security systems of this base without anyone's knowledge. I could use all the security cameras to make sure no one knew I was spying. I looked around and found the new metal plating on Miranda's workbench ready for implantation. After that I could use the overload fists without any harm to myself. I got the idea from the krogan war hammer in Mass Effect 3 multiplayer, I mean why not use my hands since I'm basically a freaking terminator. I haven't been able to find Shepard's body at all I guess they keep her in a special area that doesn't have security cameras. Alpha told me Miranda was on her way back so I quickly jumped up onto her workbench simply to annoy her.

"Shaun how many times have I specifically told you not to sit on my workbench." I shrugged at her and smiled. If there was anything that I actually enjoyed at this station it was annoying Miranda god knows it's not the food that they give me or the company they make watch me. "I see you've found your new armor plating, it's a lot tougher than your current one. You'll be able to use that overload fist that you used doing your combat simulation without injuring yourself. There is one drawback though the armor is heavier so you will move slower, but I'm sure with more training with Jacob that you'll be moving faster in no time." _I hate Jacob with a burning passion; first of all I just hate his character I can't stand him. Second he's my physical trainer and he puts me through hell every freaking day. I don't even think he's human nobody does that many pushups in one go like what the hell?_

I lay down and Miranda began to remove my current armor plating and made quick work to replace them with the new ones. As soon as she started to place them into the slots I could instantly feel the increase in pressure, this is going to be a pain to deal with. "Shaun I'm going to sedate you for this next part." I nodded and closed my eyes. Just because my body was sedated didn't mean my mind was. Basically my body shuts off, it gives it time to rest and I can choose to rest with it or I can chose to talk to Alpha.

'_What do you think of the new plating Alpha? Think we'll be able to use more of the techniques that I've been thinking of?' _

'_It will be difficult to cloak with this new plating, but it should not pose any immense problems. As for your techniques you will now be able to use overload fist, cryo fist, and the pyro fist with ease.' _

'_That's great; I need to be ready for when Shepard wakes up. I'm bringing a whole new skill set to the table, but I kind of miss being able to talk.' _

'_That will soon be remedied.' _

'_What are you talking about?' _

'_Ms. Lawson sedated you without informing you that she will be implanting a voice chip into you.' _

'_You mean I'll be able to talk again that's amazing. As soon as I wake up I'm hugging Miranda whether she wants it or not.' _

'_We advise against such an action.' _

'_Whatever Alpha I'm sure it'll be fine.'_

* * *

God I shouldn't have hugged Miranda. She didn't take my hug to well and decided that kneeing me in the nuts was the proper response. I may have armor plating but that still hurt. _'We believe the saying is we told you so.' _

'_Shut up.' _I got up off the ground after being kneed in the nuts and had to go meet Jacob for physical training. I still feel kind of sick to my stomach, god I'm going to throw up all over Jacob.

"I'm here Jacob." I said in my new mechanized voice. _'Alpha can you optimize the voice chip so I sound like I would normally?' _

'_We can do that.' _

'_Great so you'll do it?'_

'_We did not say that. We believe your current voice is quite sexy as Traynor referred EDI's voice to be.' _

'_Alpha there are two things wrong with that statement, first thing is I don't want to sound like EDI because I'm a guy. Second if you don't stop being such a smartass I'm going to stop letting you look into my memories.' _

'_We believe that statement is a lie.'_

'_Fine you got me I'm still going to let you into my memories, just change the voice ok?' _

'_We will do so.' _I coughed saying a few words to make sure that Alpha didn't make me sound like a woman.

"Looks like you got your voice back, but that's not going to help you with your training. Miranda tells me that you got new armor plating and you need to increase your speed so one hundred laps around the track." Jacob said with a smirk. _I hate you so much Jacob, one of these days during sparring I'm going to wipe the floor with you. _

After my hundred laps I was done for the day, but that didn't stop Jacob from pestering me. "Do you know why you had to run one hundred laps instead of your normal ten?"

"Is it because I hugged Miranda?"

"Got it in one she wanted you to be punished for that." Jacob pointed to the viewing area "She's been drinking tea and watching you suffer the whole time."

"Great I won't hug here anymore; glad that's over with now can I go rest." I tried to move past Jacob but he put his arms in front of me to stop me.

"No what you're going to do is go apologize to Miranda." I looked at him he can't be serious right.

"You're joking right?"

"Does it look like I'm joking?" He crossed his arms and gave me a look.

"You want me to apologize for giving her a hug? You're out of your mind; now get out of my way before I make you."

"Try it." I made the armor plating appear on my right hand and aimed my fist at Jacob's face but before I could hit him my fist stopped in its tracks.

"I think that's enough testosterone for today don't you think boys?" I looked over to see Miranda walking up holding a remote in her hands. "Now Shaun why don't you head on over to your room and stay there the rest of the night." She hit the remote and my body started moving on its own.

'_Alpha why do we have to act like we're being controlled again, I really wanted to punch Jacob in the face.' _

'_For our plan to work we must make it seem as if we are still under TIM's control. If he realizes that we are not he will have us terminated.'_

'_Yeah I know you're right I just really wanted to punch him in the face.'_

'_There will be many opportunities for that down the road.' _

'_Promise?'_

'_We will make sure to place you in many situations where causing Jacob bodily harm is looked on as good.' _

'_Great what more can I ask for.' _

* * *

The next three months passed relatively quickly, my training regimen was increased exponentially since I was implanted with my new armor. TIM decided that stealth training was also imperative for me to know so I was equipped with the most up-to-date cloak it was similar to that of the Phantoms. He also decided that learning how to use a sword would be helpful. Looks like I'll be learning how to use an electric slash; this is going to be useful. The day Shepard awoke I was already set to escape, I found Jacob and Shepard fighting LOKI mechs and they were pinned down.

"Jacob! Shepard! Duck now!" I yelled at them as I sent an electric slash at the mechs causing them to short circuit and explode. "Jacob what happened?" _I already knew what happened but appearances. _

"The mechs just started going crazy and shooting at everyone, have you heard from Miranda?"

"I just got out of my room and realized the mechs were going crazy, I'll get Alpha to find Miranda." I closed my eyes. _'Alpha is Miranda still near the shuttle area?' _

'_She is currently heading to the shuttle area and has met little resistance; Wilson has already been shot and is currently bleeding out.' _

"She's heading to the shuttle area, we should meet her there. Let's go." I said

"Wait I'm not going anywhere with you two until you tell me what's going on." I looked at Jacob and could tell he wasn't talking which meant that I had to.

"You've been dead for a couple of years Shepard; we brought you back from the dead, well technically Miranda brought you back."

"What happened to the Normandy? Where's my old crew?" She asked me moving towards me somewhat aggressively.

"The Normandy was destroyed in the attack, as far as I know Kaidan Alenko survived the attack." Jacob looked at me as if I knew too much; I would have to deal with him latter. "Look Shepard you have no reason to trust us, but right now we're your best chance on getting off this base alive. So whether you like it or not we have to work together, if you want to shoot Jacob later you can." Jacob gave me a death stare and I shrugged it off.

'_Shaun, Miranda has made it to the shuttle area during the time of your conversation.' _

'_Thanks Alpha you're the best.' _

'_This is common knowledge.'_

"Alpha says Miranda has made it to the shuttle area we should head there now."

Shepard looked at me curiously, "Who's Alpha?"

_I was hoping to prolong this conversation. _"Alpha is the geth intelligence in my head; I'm an experiment of an organization that specializes in experimental technology." She looked at me in disbelief, she couldn't believe that someone would implant geth technology into a human.

"What's the name of this organization?" I then noticed more mechs were entering the room and pushed Shepard towards Jacob.

"Get her out here Jacob, I'll hold them off. I'll meet you at the shuttle area." He nodded and the two headed out. I quickly ducked behind cover. _'Alpha what is the approximate time till Shepard reaches Miranda?' _

'_Approximately 30 minutes till they reach their destination.' _

'_How long will it take us to deal with all the mechs?' _

'_It should take approximately 20 minutes, and then we will be able to reach the shuttle area in 10.' _

'_Alright let's get started.' _

* * *

I stayed behind cover and used the security cameras to gain the locations of all the mechs. Only about 10 mechs, damn this could take longer than expected. It looks like they all have armor on, wait armor that means crap INSANITY. Well might as well get to it, if I die on here then I'll be no help to Shepard. I have all the locations of them in my mind; the trajectories are being drawn up. I can't get to close or else they'll shoot me dead no matter how powerful my armor is. I grabbed the hilt of my sword and charged it with electricity and fire. I'll use the fire to burn away the armor and the electricity to short circuit them. It's quite difficult to use two abilities at once now I know why it was never done in the game. I jumped from out of cover and slashed at half of the LOKI mechs sending a wave of fire and electricity at them. I was able to take out half of them, and then I hid behind cover once again. God my hand, it hurt it wasn't supposed to hurt that's why I got the new armor. _'Shaun it is unwise to use two abilities, our current armor cannot sustain the damage. We estimate that your right hand has a second degree burn; we are dispatching nanobots to fix the injured area. Please refrain from using such harmful techniques during this battle.' _

'_Alright I was being stupid, sometimes I forget that this is all real I won't forget that again.' _

At least I only had 5 mechs to deal with, but I have to not use my right hand until it's healed. I grabbed my Carnifex pistol from my belt and shot at the mechs. Their bullets were flying past my head till I was caught in the chest pushing me back. It looked like my armor was holding up nicely hopefully it would keep holding on. Two more mechs went down from my Carnifex, only three more left. I jumped behind a box quickly as a rocket raced by my head. That was close I was almost hit in my head with a rocket, that would have been bad. I was running low on ammo; I had about one shot left. I couldn't get close to any of the mechs because of the gap. _'How's my hand doing Alpha?' _

'_It is still in the process of healing.' _

'_Any ideas on what to do here Alpha, I've got one bullet and three mechs left.' _

'_The experimental weapon is ready for use. We believe it will cause you no harm, we will draw the final trajectories so that you may defeat them.' _

'_Good I was getting worried; I knew I could count on you Alpha.'_

'_You had doubt?'_

'_No of course not, I had complete faith in you Alpha.' _

'_We call what was the word? Bullshit.' _

'_Smartass.' _

I stood from the barrier and shot my last bullet finishing off one of the mechs. I lifted up my left arm and aimed it at the remaining two mechs using my right arm to steady my left arm. "Left arm arc launcher engage." A small gun rose from my arm and launched a short electrical net that slowly extended enveloping the final two mechs. The two mechs exploded and I was finally done with all of the mechs. It was time to make my way to the shuttle area.

* * *

**A/N: Well there it is I hope you all enjoyed reading it as much as I enjoyed writing it. As I said constructive criticism is appreciated. It made sense to me that Cerberus was experimenting with geth technology since they were experimenting with Reaper technology. Hope I was able to convey it well. Favorite, Follow, Review Till Next Time.**


	2. Chapter 2

**A/N: First off let me say HOLY CRAP this blew up, second thank you all for the follows, favorites, and reviews.  
Guest: My character will be paired with someone that is not Shepard, as of right now it is only Shepard since the others have yet to be recruited.  
**

**Starspike7: I really appreciate your criticism and advice, as for why he came to terms so easily it will be explained. I plan to address everything that you have mentioned and will be able to make this story all the more better because of your review.**

**Also this story now has a beta reader which is ShadowAngel23 so expect chapter updates that will fix anything that I have missed.**

* * *

As I ran through the exploding base, and I caught glimpses of the destruction that Shepard had left in her wake. Mechanical bits and pieces were scattered around every room, and I could see that some of the pieces had been burned by biotics. I know that Jacob's biotics weren't this powerful which means that Shepard was either a vanguard or an adept, that's good to know for future missions. I thought I was fine, but I was proven wrong when I came across a window smeared with blood. The dead bodies in front of me had smeared the glass with blood. It made me sick and I'm not sure if I could handle it. I had seen bodies at funerals before, but the bodies had been punctured with bullets and they were unrecognizable as the flames enveloped their bodies. It reminds me of him.

'_Shaun we suggest continuing towards the shuttle area, if you do not it is likely that they will leave you to die.' _

'_I know Alpha, it's just…' _

'_We understand your concern, but now is not the time.' _

I know Alpha was right and I continued towards the shuttle area, as I entered I saw Shepard pointing her gun at Miranda.

"Shepard that's not a good idea." I said and moved forward, but stopped when Shepard gave me a death stare.

"I don't trust any of you; the only one that has been open to me was him." She motioned to me with her head and I could see Miranda and Jacob glaring at me.

'_Alpha did Jacob tell Shepard that this is a Cerberus base.' _

'_He did not do such a thing. We believe that our presence has changed Jacob's personality. In your universe he had redeemable qualities, now it seems like he is loyal to Cerberus.' _

I sighed, "Listen Shepard I need to tell you the whole truth." I saw Miranda move towards her pocket.

"I don't think so sweetheart." Shepard continued to point her gun at Miranda, and then Jacob drew his gun at Shepard. I responded by pointing my gun towards Jacob which received several questioning glances.

"Shepard I told you that I was an experiment made by an organization that specializes in experimental technology. This organization is known as Cerberus." Shepard eyed me while still pointing her gun towards Miranda. "Look I'm sure their boss can tell you more once we get off this base."

"Why should I trust Cerberus? The few run ins I had with your organization were not pleasant, I've seen what you can do."

I put down my gun and walked towards Shepard, "Shepard you've had many people work under you, all of them trustworthy I would say that you are a great judge of character. You decide whether you can trust me or not. If you don't then you can put a bullet in my head."

Shepard sighed and put down her gun, "Fine take me to your leader." I stopped myself from laughing. "If I don't like what I hear, don't expect to survive." Shepard walked towards the shuttle and entered leaving me with Miranda and Jacob.

"What?" I asked as they were glaring at me and I glared right back.

"You shouldn't have said anything; it wasn't for you to tell." Jacob said annoyed.

"You think keeping information from her is a good way to gain her trust? I knew you were slow Jacob, but I didn't think you were downright idiotic." Jacob moved towards me. "Try it Jacob. I'm sure Miranda has already noticed that her remote doesn't actually work." Jacob looked towards Miranda and she nodded. "Now let's go." I made my way to the shuttle but Jacob grabbed my arm.

"If you betray Cerberus or us, I will put you down." I grabbed Jacob's wrist and squeezed just enough to make it hurt before the point of breaking it. His face cringed from the pain that I was inflicting on him.

"I'd like to see you try Jacob, you're no different than all the other Cerberus lackeys. You think you're special let me tell you that you're not." I pushed him away and sat inside the shuttle next to Shepard.

"Having trouble in paradise?" She asked me obviously trying to get more information out of me.

"I didn't want to be part of Cerberus Shepard; I don't even remember how I even got on this base. All I remember is waking up in a locked room with a geth intellect inside me along with other several upgrades."

"Cerberus is monstrous; I don't understand how anyone can follow them." She gave my hand a light squeeze in understanding. "How does that whole geth intellect work?"

"Well when we first started out, he would take control of my body until I was used to it, but as time progressed and I got used to the training he took a supportive role. It's like having a supercomputer in my head constantly sending me combat data so I can draw up the most effective strategy. I have the intellect of a machine, but the instincts of a human."

"Perhaps you could refrain from revealing anymore Cerberus secrets until we get in touch with the boss." Miranda said as she entered the shuttle.

"I can reveal whatever I want Miranda, I'm not a Cerberus lackey." I snapped at her. "But I'll finish telling you the rest later Shepard." She nodded and I closed my eyes to speak to Alpha.

'_You know in the game it was all scripted, but this is real now so I have to treat everyone like real people. I know that they'll get better further down the road, but right now Miranda is hardly tolerable. She's back to being the Ice Queen and Jacob is just another uniform. I never liked Jacob, but at least he wasn't such a tool before.'_

'_We fail to see how this pertains to us.' _

'_I'm ranting to you Alpha; it's my way of airing all my thoughts out since I can't say it all out loud.' _

'_Over these past six months we have observed your behavior, and all of your memories. When you saw those bodies you froze. We believed that we had prepared you for taking lives, since that is the only way to stop the Reapers.'_

'_I know that. I tried to steel myself from it, but I've never killed a person before Alpha. I can't think of them as videogame characters. All of them are real, and each one that I will kill has a family, they are special to someone." _

"_The needs of the many outweigh the needs of the few. We believe that you know this." _

"_Yeah I know in order to protect billions of lives; I will need to take hundreds. I hope that I'm still the same person after all this is over. _

"_We will help you Shaun in this endeavor."_

"_Thank you Alpha." _

* * *

As I open my eyes I realize that we had arrived at another base and everyone had left the shuttle to go meet TIM. Well this was the moment of truth I would have to face TIM now that he knew I was free from his control. I really hope he doesn't have me killed because that would be a real pain.

* * *

"I don't trust you or your organization." Shepard said as she crossed her arms facing the hologram of TIM. She couldn't believe that he didn't at least have the decency to face her in person, granted she probably would have shoved a gun in his face had he actually shown up.

"You don't have to trust us, go to Freedom's Progress and you'll realize that we need each other."

"What about my old team?"

"Liara is currently on Illium working as an information broker it is possible she is working for the Shadow Broker if so she is not to be trusted, Garrus is unaccounted for, Kaidan is currently working undercover missions for the Alliance, and last information I received on Tali was that she was with the Migrant Fleet."

"So I should trust those you give me?"

"Miranda and Jacob will follow your orders since I have ordered them to, since Shaun has broken free from his control chip you can choose to take him with you."

"You had a control ship put inside him, wasn't putting a geth in his head enough! God knows what other upgrades you've given him, he's probably not even human anymore."

"You fail to see that he is the epitome of coexistence between human and synthetic. He still remains human his consciousness is what allowed him to break free from the control chip. As for his upgrades his blood was replaced with upgraded nanobots. Nanobots are primarily used to heal injuries, but we have found a way to weaponize them. Our scientists upgraded the nanobots to take in metal constructs and they will be able to recreate them."

"What exactly does that mean?" Shepard asked curiously.

"His body is his armor. The nanobots in his blood excrete from his skin creating armor plating in order to protect him. This can also be used for weapons, but he has only been able to create one weapon so far."

Shepard nodded in understanding, "I'll head to Freedom's Progress but I make no promises."

"Very well Shepard."

* * *

TIM was not happy with the way that his meeting with Shepard played out. He had hoped that she would be more understanding but that didn't happen. The fact that Shaun had broken free from his control chip and Shepard knew was going to cause more problems. He had to make sure that Shaun wasn't going to become more trouble than he was worth.

* * *

I waited nervously for Shepard to finish her meeting with TIM; I hope that it would go decently. It would be great if Shepard told TIM to go screw but I hope that she would stick to the storyline. I mean it would be bad if she decided to not even bother with Freedom's Progress. I don't even think that's possible, I mean if it did that would screw things majorly. I need to make sure everything stays on track if I'm going to save as many people as I can. I cannot make it seem like I know too much or everyone will get suspicious. I can only imagine what TIM could do with my foreknowledge.

The ride to Freedom's Progress was fairly short and boring if not for Alpha's decision to start rambling off multiple scenarios that could occur on Freedom's Progress I most likely would have fallen asleep. This would be my first time seeing Tali, but if I recall right she gets slightly pissed off at seeing Cerberus. We made quick work of all the mechs leading up to where Tali and the other quarians were located. I have to admit that Tali looked amazing in her suit; I know Rob would have a fit if he could see her. The scene played off like it did in the game except it wasn't as scripted and there were a few more curse words thrown. Judging by how Shepard has been acting she's a mix of renegade and paragon. I would have to help her lean toward paragon and the important moments.

"Perhaps it would be best if we split our groups up?" Miranda suggested to Shepard and Tali.

"There are two entrances to where Veetor is located; we will take the west entrance while you take the east." Tali replied. Tali's group didn't look to happy about working with Cerberus, but Tali had made it clear to them that she trusted Shepard.

"Sounds like a plan." Shepard nodded and our two groups split up. We headed down when all of a sudden rocket drones flew by us and started to unload on us. We quickly ducked behind the scaffolding to avoid their fire. Shepard fired off a few shots and then we realized that all the drones had shields up. "Shaun overload their shields." I nodded and grabbed the hilt of my sword infusing it with electrical energy and slashed a wide enough area to reach all of the drones. As their shields went down Shepard unleashed a powerful shockwave destroying everything in its pathway.

"Shepard I tried to make them wait but they went on ahead. You need to hurry their getting torn apart." Tali radioed. _Crap if we don't hurry then they're all going to die. What good is my being here if I can't save lives?_ I race ahead of Shepard and the rest of the group.

"Shaun what the hell are you doing stay in formation?" Shepard yelled at me. I ignored her knowing that I would get it later. I unlocked the door to find the YMIR mech shooting rockets at the quarians.

"All of you get to cover I'll get its attention." I yelled at the remaining two quarians. They ran to cover, but not before the mech clipped one of the quarian's legs causing her to fall to the ground. I ran towards the quarian and slammed my fists in the ground creating an electrical shield around myself and the quarian. Bullets were pounding on the shield and it was only a matter of time before they ripped through.

"Why are you doing this?" The quarian looked at me questioningly. Was she really asking this?

"Because I'm not going to let anyone die if I can save them." I smile at her as the sounds of bullets roared through the air. I wave my hand on her leg applying what little medigel I had with me. "Can you move your leg?" She nodded. "Good that means you can run. My shields are about to drop, but I'll buy you some time."

"Thank you." She replied, I nod and signal for her to get ready. I turned to the YMIR mech as my shield dropped and raised my left arm and steadied it with my right. "Left arm arc launcher engage." My gun rose from my left arm and crackled intensely; it shot out completely overloading the mech's shield. The mech shot out a rocket and it nailed me straight in the chest knocking me back into a building. The mech was about to shoot me once more when a blue orb came out of nowhere slamming into the mech chipping its armor. I looked towards the direction of the entrance and saw Shepard, Jacob, and Miranda firing at the mech. Shepard motioned for Jacob and Miranda to get the mech's attention and she raced towards me.

"Shaun are you okay?" She held up her hand applying medigel.

"I'll be fine." I coughed out. "The rocket hit my chest but my armor was able to slow it down before it punched a hole through my body."

"Good now stay down while we deal with the mech, and don't think I forgot about you breaking formation." Shepard went back to the fight and the three of them finished the mech fairly quickly with a three pronged biotic attack.

'_Alpha the quarians are they alive?'_

'_Yes the two quarians are currently alive; we believe that they have received no serious afflictions.'_

'_That's good I'm glad I was able to save them.' _

* * *

I was able to stand and I limped with Shepard and the rest of the group towards Veetor. He was going insane, he kept mumbling until Shepard turned off the monitors using her omnitool. _Good paragon interrupt. _

"What happened here?" Shepard asked Veetor.

Veetor held his head, "They came, it was so dark, and they took everyone." He began to shake as the video of the Collectors began to play.

"He's not making any sense Shepard we should take him in for more information." Jacob suggested.

"Shepard no, you don't know what Cerberus will do to him." Tali said frantically "You can have his omnitool it should have all the data he was able to get."

"I agree with Tali Shepard, Cerberus isn't the type to play nice when trying to obtain information. If anything they'll scar Veetor more than he currently is." I said and saw Tali giving me a look that said thank you.

"We should take him in his information could prove useful." Miranda let out. Shepard looked like she was getting frustrated.

"Enough Veetor will return with Tali and I don't want to hear any more about this." Shepard yelled.

"I don't think that's such a good idea Shepard. TIM won't be too happy about this." Jacob replied.

"Well I don't care what you or TIM thinks." Shepard snapped.

* * *

I was getting tired of this argument and decided to wait outside by the shuttle. "Hey." I look over to see the quarian that I saved. "I wanted to thank you for saving my life and my friend's life. The name's Raleya vas Neya"

"Pleasure to meet you Raleya and it was no problem; I would have done it for anyone." I replied.

"Not many humans are like you. You're accepting when most tend to be more racist towards us saying that we're thieves and blaming us for the geth."

"Those people are idiots; you can't keep blaming others for past mistakes. I accept all people no matter what their race is." I look to see Shepard signaling me that it was time to leave. "Looks like it's time for me to head out. It was nice to meet you Raleya vas Neya, I hope to meet you again soon. My name's Shaun by the way."

* * *

We arrived at the Normandy Sr-2 in a few hours and I headed to the second floor. It was a lot larger than in the game and there were more rooms than were let on in the game. I chose an empty room in between Thane and Kasumi. It was about the size of Kasumi's room, but it didn't have a view. I start to unpack what little luggage I had and laid on my bed. I stared up at the ceiling and think about what's going to happen. There are so many factors that I'm going to have to deal with. How am I going to keep everything on track? How can I stop them all from dying? I close my eyes and let sleep envelop me for the first time in months.

* * *

_I'm running down a hallway there's no doors and no windows, where the hell am I? What is that horrible smell? Why does this hallway feel endless? That smell it's getting closer, wait I see a turn. No why is this happening? I kneel down on the floor when I realize what the smell was. The bodies on the base, they're all in front of me. Why are their eyes open? Why are they looking at me? Their mouths are moving, no that's not possible their dead. Their trying to speak but no words are coming out. I grab my head as the hallway fills with screams, but it's not coming from the bodies it's coming from me. The bodies are mouthing "Why didn't you save us? Why?" No please this isn't right, it has to be a dream. Why can't I wake up? _

* * *

I scream myself awake and find myself in my bed shaking. I held out my hand it wouldn't stop moving, I tried to grab the glass of water that was on my desk. I was able to grab a hold of it but when I brought it to my lips I had shaken the glass so furiously that all the water was gone. _Damn it why is this happening again?! _I threw the glass against the wall shattering it. _I tried so hard to keep it all bottled in, but my emotions keep leaking through. The bodies I can't get them out of my head. _

'_Shaun would you like us to perform the procedure once again?' _

'_Alpha I thought I would be fine why am I feeling this way?' _

'_The procedure we performed was temporary; we believe that seeing a dead body and the quarians being killed unlocked the lock we placed on you.' _

'_I need this, I need this to grow. I wanted it to all be a game; I made you lock away parts of myself so it all seemed more normal. Everything is rushing back in Alpha, it hurts so much. I feel like my head is going to explode.'_

'_We can slow the progress so it will not hurt.' _

'_No, I've turned a blind eye to the reality of my situation, I need it all Alpha. Unlock it all.' _

'_Are you sure? The process will be extremely painful and we do not yet know the side effects that it will have.' _

'_Do it Alpha and lock the door. I don't want anyone coming in; I don't know what I'll do when all of it comes back.' _

'_Affirmative, process will begin in 3, 2, and 1.' _

I grabbed my head as the pain started flowing in; I slammed my head against the wall and began to see blood. Whose blood is it? My hand moved to my head, it's my head. I'm bleeding, but why am I hearing laughing? It's me why am I laughing? It still hurts like a thousand needles are pushing against my skull trying to escape. Am I laughing to hide the pain? It hurts so much I don't think I can stay awake for much longer. The pain is so unbearable; I've never felt pain so intense that I just wanted it to end. I wanted everything to end. Images are flashing in my head.

* * *

**Flashback**

Cold metal hands in front of my face as I stared down, what did I do? Cold steel pounding against flesh breaking bones, blood splattering across my face. I look at his face, is that his face I can't even tell anymore. Why did I do this? Who am I? My body why did it move on its own, I wanted to stop. My fists moved all by themselves why? Why? Why? This is a game right? It'll be fine when I close my eyes it'll all disappear. I shut my eyes, it'll be gone please be gone. No! Why am I still here? My eyes start to water, and I feel myself slipping into unconsciousness.

"It worked wonders didn't it sir." The scientist said showing TIM the video of what exactly the control chip did. "He wasn't able to stop, and with this chip he will follow your every command."

TIM looked at the video and smiled, it was perfect. He had the ultimate soldier one that would obey without question. "It is quite impressive Mr. Archer, this is quite the achievement."

"Thank you sir if there is anything else that you need?"

"No that will be all, you may return to your other projects for now." TIM waved his hands allowing Archer to leave. TIM couldn't hide his smile when watching the video of Shaun beating the man to a bloody pulp. The man was an Alliance spy inside of Cerberus, the Alliance should know better than to mess with affairs that were beyond them. The things he could do with his soldier.

I haven't stopped crying not since I killed him. I don't even know his name; his face is just a bloody pulp. That's all I can see now, his smashed in face. I clawed at my head trying to get it out.

'_Shaun we believe the best course of action would be to calm down.' _

'_I just killed someone how the hell can I come down? Nothing is normal anymore; I'm stuck in a game. Why did I do it?' _

'_You were implanted with a control chip so that TIM could use you the way he sees fit. We were unable to disrupt the chip before you received the order to kill that man. We can now destroy the chip to avoid further control.' _

'_Do it! Do it now!' _

'_Understood we will begin the process.' _

'_I can't get the images out of my head Alpha. Please help me.' _

'_We will do what we can, but it may not be pleasant.' _

'_I don't care just do it.' _

My mind went blank everything just seemed to be put into perspective. I'm in a game and my mission is to save as many people as possible. I will do what I must to survive and help Shepard. My life is a game, and I know what I must do.

**End Flashback**

* * *

I opened my eyes and most of the pain had subsided but my head still felt like needles were pushing through my temple. I regained everything; all of it had come back. My guilt, my anger, and my sorrow everything had returned after hours of excruciating pain.

'_The process has been finished, but as we stated before we do not know what side effects may occur.' _

'_I killed someone; I murdered someone with my hands.'_

'_You were not in control of your bodily functions; it is not your fault.'_

'_It was still my body; I should have been strong enough to resist the control.' _

'_Before entering this universe you were a normal person. It is not likely that you would have been able to resist such technology.' _

'_I don't care, I should have been stronger. I know what I did; I know what I have to do. I'm going to save everyone and kill TIM. He made me into his personal killing machine. He's going to get exactly what he wanted.' _

* * *

**A/N: Alright there you have it the second chapter of Alpha. I hope you all enjoy it, if you have any questions just review and I'll answer them in the next update. Also I mentioned in the above note that this story was being beta read once a chapter has been read and edited it will have this at the bottom.  
(_Beta read by ShadowAngel23) _So you all know what to look out for. Well I'll leave you to it. Read, follow, favorite, or review. Till Next Time.**


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